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Identification of EV-responsive transcripts in the planarian Schmidtea mediterranea

ABSTRACT: The roles of extracellular vesicles in animal models of regeneration are poorly characterized. The goal of this study was to identify differentially expressed transcripts in planarian flatworms after injection of buffer only or extracellular vesicles compared to uninjected animals.

ORGANISM(S): Schmidtea mediterranea

PROVIDER: GSE261722 | GEO | 2024/10/01

REPOSITORIES: GEO

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HOX gene complement and expression in the planarian Schmidtea mediterranea

Project description:Background: Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results: Because the planarian Schmidtea mediterranea (S. med) is unsegmented, appendage-less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here we argue against this hypothesis and show that S. med has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly-sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially-restricted expression. Finally, we confirm HOX gene axial expression by RNA-deep-sequencing 6 anterior-to-posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially-restricted transcripts. Conclusions: Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.

2016-03-08 | GSE78937 | GEO

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea

2011-07-15 | E-MTAB-607 | biostudies-arrayexpress

Cell type transcriptome atlas for the planarian Schmidtea mediterranea

Project description:The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.

2018-04-17 | GSE111764 | GEO

RNA sequencing of pole-containing anterior tip regions in planarian Schmidtea mediterranea

Project description:RNA sequencing identified new anterior-pole enriched genes encoding transcription factors, a secreted protein, and a transmembrane protein, including NR4A, a nuclear receptor gene that is important in patterning the planarian head and tail.

2019-05-25 | GSE121045 | GEO

Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea

Project description:Investigation of differences in gene expression between two strains of the planarian Schmidtea mediterranea. The sexual strain are cross-fertilizing hermaphrodites with reproductive organs that develop post-embryonically and the asexual strain reproduces exclusively by transverse fission and fail to develop reproductive organs. A two chip study using total RNA recovered from asexual and sexual animals. Each chip measures the expression level of 16,797 ESTs from S. mediterranea with 10 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

2011-11-01 | E-GEOD-32450 | biostudies-arrayexpress

RNA sequencing of single cells from the midline posterior extremity in planarian Schmidtea mediterranea

Project description:RNA sequencing of single cells from the midline posterior tip of the tail and posterior blastema in planarian Schmidtea mediterranea identified new posterior-pole enriched genes

2019-05-25 | GSE121047 | GEO

Transcriptional profiling of laser captured intestinal tissue from the planarian Schmidtea mediterranea

Project description:Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.

2020-03-20 | GSE135351 | GEO

Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea

2011-11-01 | GSE32450 | GEO

The head-regeneration transcriptome of the planarian Schmidtea mediterranea.

Project description:BACKGROUND: Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. RESULTS: To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. CONCLUSIONS: Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.

| S-EPMC3245616 | biostudies-literature

Neoblast specialization in regeneration of the planarian Schmidtea mediterranea.

Project description:Planarians can regenerate any missing body part in a process requiring dividing cells called neoblasts. Historically, neoblasts have largely been considered a homogeneous stem cell population. Most studies, however, analyzed neoblasts at the population rather than the single-cell level, leaving the degree of heterogeneity in this population unresolved. We combined RNA sequencing of neoblasts from wounded planarians with expression screening and identified 33 transcription factors transcribed in specific differentiated cells and in small fractions of neoblasts during regeneration. Many neoblast subsets expressing distinct tissue-associated transcription factors were present, suggesting candidate specification into many lineages. Consistent with this possibility, klf, pax3/7, and FoxA were required for the differentiation of cintillo-expressing sensory neurons, dopamine-?-hydroxylase-expressing neurons, and the pharynx, respectively. Together, these results suggest that specification of cell fate for most-to-all regenerative lineages occurs within neoblasts, with regenerative cells of blastemas being generated from a highly heterogeneous collection of lineage-specified neoblasts.

| S-EPMC4176530 | biostudies-literature

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